Biocview "SNP"

Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization
Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization
A Genetic-Based Assay for the Identification of Cell Lines
A Genotype Calling Algorithm for Affymetrix SNP Arrays
Analysis of Large Affymetrix Microarray Data Sets
Analysis of Large Affymetrix Microarray Data Sets
Analysis of Parent-Specific DNA Copy Numbers
Analysis of Parent-Specific DNA Copy Numbers
Analytical Tools for MassArray Data
Ancestry Specific Allele Frequency Estimation
Ancestry Specific Allele Frequency Estimation
Annotation of Genetic Variants
Annotation of Genetic Variants
Annotation of Genetic Variants
An R package for analysis of case-control studies in genetic epidemiology
An R package for computing the number of susceptibility SNPs
An R package to identify multi-snp effects in nuclear family studies using the GADGETS method
A Package for De Novo CNV Detection in Case-Parent Trios
A Package for De Novo CNV Detection in Case-Parent Trios
A package for variant peptides detection and visualization in shotgun proteomics.
appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV
appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV
A RangedSummarizedExperiment with methods for copy number analysis
Asessing statistical significance in predictive GWA studies
Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations
Bayesian analysis of Gaussian GWAS data
Bayesian Piecewise Constant Regression for DNA copy number estimation
Bayesian Piecewise Constant Regression for DNA copy number estimation
BBCAnalyzer: an R/Bioconductor package for visualizing base counts
Bioconductor components for general cancer genomics
Bioconductor components for general cancer genomics
Candidate Gene Miner
Candidate gene prioritization based on convergent evidence
Candidate gene prioritization based on convergent evidence
Candidate gene prioritization based on convergent evidence
Candidate gene prioritization based on convergent evidence
Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations
CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.
Comprehensive QTL annotation of GWAS results
Comprehensive QTL annotation of GWAS results
Comprehensive QTL annotation of GWAS results
Copy-Number Analysis of Large Microarray Data Sets
Copy-Number Analysis of Large Microarray Data Sets
Correlated Meta-Analysis
data structures for linkage disequilibrium measures in populations
data structures for linkage disequilibrium measures in populations
Decomposition of individual tumors into mutational signatures by signature refitting
Decomposition of individual tumors into mutational signatures by signature refitting
Detection, Characterization and Visualization of Kataegis in Sequencing Data
Detection of site fixation in molecular evolution
Detection of subclonal SNVs in deep sequencing data.
Detection of subclonal SNVs in deep sequencing data.
Detection of subclonal SNVs in deep sequencing data.
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
Dual redundant reference sequencing
Dual redundant reference sequencing
Error correction tool for noisy genotyping by sequencing (GBS) data
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
Filtering of coding and non-coding genetic variants
Filtering of coding and non-coding genetic variants
Find SNV/Indel differences between two bam files with near relationship
GEM: fast association study for the interplay of Gene, Environment and Methylation
GEM: fast association study for the interplay of Gene, Environment and Methylation
GEM: fast association study for the interplay of Gene, Environment and Methylation
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search
Generate customized protein databases from NGS data for proteomics search
Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences
GeneRegionScan
genesis assocation testing code rewrite
genesis assocation testing code rewrite
Genetic Algorithms for Understanding Clonal Heterogeneity and Ordering
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
Genomic Knowledge-guided Multiple Testing
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
Genotype Conditional Association TEST
Genotype Conditional Association TEST
Genotype Imputed Gene Set Enrichment Analysis
Genotype Imputed Gene Set Enrichment Analysis
Genotyping and QTL Mapping in DO Mice
Genotyping and QTL Mapping in DO Mice
Get inversion status in predefined regions
Get inversion status in predefined regions
Get inversion status in predefined regions
Get the QTL/gene/SNP data functions
Gimpute: An efficient genetic data processing and imputation pipeline
gin in R
gin in R
GPA (Genetic analysis incorporating Pleiotropy and Annotation)
GPA (Genetic analysis incorporating Pleiotropy and Annotation)
gQTLBase: infrastructure for eQTL, mQTL and similar studies
gQTLstats: computationally efficient analysis for eQTL and allied studies
graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture
GWAS-based Mendelian Randomization and Path Analyses
GWAS-based Mendelian Randomization and Path Analyses
GWAS for Selfing Species
GWAS for Selfing Species
GWAS Incorporating Networks
GWAS Incorporating Networks
gwasurvivr: an R package for genome wide survival analysis
gwasurvivr: an R package for genome wide survival analysis
gwasurvivr: an R package for genome wide survival analysis
hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data
Hierarchical Inference
Hierarchical Inference
High-Throughput Sequence Analysis using the Aroma Framework
iASeq: integrating multiple sequencing datasets for detecting allele-specific events
Identification of candidate genes associated with genetic variation
Identification of candidate genes associated with genetic variation
Identification of genetic Variants affecting Alternative Splicing
Identification of SNP Interactions
Identification of SNP Interactions
Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation
Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation
Inference of Chromosome-length Haplotypes using Genomic Data of Single Gamete Cells
Inference of Chromosome-length Haplotypes using Genomic Data of Single Gamete Cells
Inference of Chromosome-Length Haplotypes Using Genomic Data of Single Gamete Cells
Infrastructure for Biostrings-based genome data packages
In-silico methods for genetic finemapping in inbred mice
In-silico methods for genetic finemapping in inbred mice
In-silico methods for genetic finemapping in inbred mice
integrated Bayesian Modeling of eQTL data
integrated Bayesian Modeling of eQTL data
Integrated Copy Number Variation detection
Integrated Copy Number Variation detection
Integrating Multi-Omic Network Data With Summay-Level GWAS Data
Integrative analysis of Multi-omics data for Alternative Splicing
Integrative analysis of Multi-omics data for Alternative Splicing
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Integrative Statistics of alleLe Dependent Expression
Integrative Statistics of alleLe Dependent Expression
Inversions in genotype data
Iterative Pruning to Capture Population Structure
Iterative Pruning to Capture Population Structure version 2
Logistic Factor Analysis for Categorical Data
Logistic Factor Analysis for Categorical Data
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data
Mapping, quantification and variant analysis of sequencing data
Mean Alterations Using Discrete Expression
Metabolomic Quantitative Trait Locus Mapping for 1H NMR data
Metabolomic Quantitative Trait Locus Mapping for 1H NMR data
Multiple Testing using SAM and Efron's Empirical Bayes Approaches
Normalization and reporting of Illumina SNP bead arrays
Objective Assessment of Copy-Number Estimates
Optimal p-value weighting with independent information
Optimal p-value weighting with independent information
Parallel implmentation of bounded memory GEE
Perform Chromosomal Ancestry Differences (CAnD) Analyses
Phylogeny-based sequence clustering with site polymorphism
Phylogeny-based sequence clustering with site polymorphism
Post-normalization of total copy numbers
Post-normalization of total copy numbers
Preprocessing tools for oligonucleotide arrays
Preprocessing tools for oligonucleotide arrays
Preprocessing tools for oligonucleotide arrays
Preprocessing tools for oligonucleotide arrays
Preprocessing tools for oligonucleotide arrays.
Processing Various Types of Data on GEO and TCGA
QA/QC of a gVCF or VCF file
QA/QC of a gVCF or VCF file
Query data from SNPedia
Representation and manipulation of short genomic alignments
Representation and manipulation of short genomic alignments
'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog
'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog
R Interface to Ensembl Variant Effect Predictor
R Interface to Ensembl Variant Effect Predictor
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R package for RIVER (RNA-Informed Variant Effect on Regulation)
R package for RIVER (RNA-Informed Variant Effect on Regulation)
R package for RIVER (RNA-Informed Variant Effect on Regulation)
Segmentation of single- and multi-track copy number data by penalized least squares regression.
Segmentation of single- and multi-track copy number data by penalized least squares regression.
Segmentation of single- and multi-track copy number data by penalized least squares regression (with hg38 and mm10).
Semi-Supervised Mixture Model
Semi-Supervised Mixture Model
Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations
SnpMatrix and XSnpMatrix classes and methods
SnpMatrix and XSnpMatrix classes and methods
software and data for analyses in genetics of gene expression
Software infrastructure for efficient representation of full genomes and their SNPs
Software infrastructure for efficient representation of full genomes and their SNPs
Standardise summary statistics from GWAS
Summarization and expression/phenotype association of CNV ranges
Summarization and expression/phenotype association of CNV ranges
Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis
Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis
systemPipeRdata: Workflow templates and sample data
systemPipeR: NGS workflow and report generation environment
systemPipeR: Workflow Environment for Data Analysis and Report Generation
Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
The data package associated with the MAGAR R-package
The 'snp.matrix' and 'X.snp.matrix' Classes
The subREgion-based BurdEn Test (REBET)
Tools for building SNPlocs data packages
Tools for Genome Wide Association Studies
Tools for Genome Wide Association Studies
Tools for Genome Wide Association Studies
Tools for Sanger Sequencing Data in R
Tools for Sanger Sequencing Data in R
Tools for Testing Gene-Gene Interaction at the Gene Level
Tools for variant data
Tools for variant data
Transcriptional Regulatory Inference from Genetics of Gene ExpRession
Transcriptional Regulatory Inference from Genetics of Gene ExpRession
Transcriptional Regulatory Inference from Genetics of Gene ExpRession
Validating Sample Identiy Through RNA-seq and DNA Genotyping Correlation
Validating Sample Identiy Through RNA-seq and DNA Genotyping Correlation
Validating Sample Identiy Through RNA-seq and DNA Genotyping Correlation
Visual comparison of mutational processes in a set of tumors
Visualizations for copy number alterations
visualize genome-wide association study with gene annotation and linkage disequiblism